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- PDB-2fqx: PnrA from Treponema pallidum complexed with guanosine -

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Basic information

Entry
Database: PDB / ID: 2fqx
TitlePnrA from Treponema pallidum complexed with guanosine
ComponentsMembrane lipoprotein tmpC
KeywordsTRANSPORT PROTEIN / ABC transport system / ligand-binding protein / guanosine / TmpC / tp0319
Function / homology
Function and homology information


ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE / Membrane lipoprotein TmpC
Similarity search - Component
Biological speciesTreponema pallidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Tomchick, D.R. / Machius, M. / Norgard, M.V.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The PnrA (Tp0319; TmpC) lipoprotein represents a new family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC)-like operon in Treponema pallidum
Authors: Deka, R.K. / Brautigam, C.A. / Yang, X.F. / Blevins, J.S. / Machius, M. / Tomchick, D.R. / Norgard, M.V.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane lipoprotein tmpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3422
Polymers34,0591
Non-polymers2831
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.855, 68.950, 69.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Membrane lipoprotein tmpC / Membrane protein C / 35 kDa antigen / Lipoprotein TpN35 / Tp0319 / TmpC / PnrA


Mass: 34058.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema pallidum (bacteria) / Gene: tmpC / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P29724
#2: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2005
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→36.9 Å / Num. all: 29393 / Num. obs: 29393 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PnrA as purified from E. coli

Resolution: 1.7→36.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1499151.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 837 2.8 %RANDOM
Rwork0.182 ---
all0.183 29375 --
obs0.182 29375 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6248 Å2 / ksol: 0.335648 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2---4.88 Å20 Å2
3---6.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 20 234 2717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.841.5
X-RAY DIFFRACTIONc_mcangle_it2.552
X-RAY DIFFRACTIONc_scbond_it3.112
X-RAY DIFFRACTIONc_scangle_it4.612.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 130 2.7 %
Rwork0.245 4637 -
obs-4637 95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3gsn_drg.param

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